The Pokemon Universe is screwed
by ZealousZorro
Summary: Master Chief and Cortana get sucked into the Pokemon Universe and they will make things go boom. Though can they do it with what Arceus gave them? HIATUS
1. A New Ending

Screwed

Chapter 1

Disclaimer: I do not own Pokemon or Halo. If I did neither would be as badass as they really are.

A ship floated almost aimlessly in space. Although it was actually just the aft of a ship floating with only two intelligences. Master Chief, inside his cryotube and Cortana barely hanging on and on the brink of rampancy.

'Three years,' Cortana thought, 'three years since we escaped the Ark and not a thing has happened.

A few thousand kilometers away from the floating aft opened up a tear in space, contrasting and almost acting on what Cortana just thought … It was not that unlike the Slipspace portals found in this universe but then this universe has shown the weird, the horrible, and the badass. When Cortana noticed said portal she immediately noticed three things wrong with this.

One, it was tinged the regular dark blue as well as _pink. _Two, the sensor readings for the portal were off the scale and holding little in common with a typical Slipspace portal. The third and final thing that was wrong was that there was nothing around to have made the portal. Worst of all the aft of the _Forward Unto Dawn _was on a direct course with the portal with no chance of avoiding up.

All Cortana could do was start the awakening procedures on the Chief's cryotube. The last thoughts Cortana remembered before she disappeared into the portal was 'Damn, I still owe the Arbiter twenty bucks for making it off the Ark alive.

A/N: This was just a compelling idea to me because it answers the question of 'How can Pokemon be more badass than its happy-go-lucky self?' The only thing I can assure you about this story is that Master Chief will kill Pokemon, Master Chief will become a badass Pokemon trainer, and that Master chief will get some badass Pokemon throughout his journey.


	2. Second Contact

CHAPTER 2

Disclaimer: I do not own Pokemon or Halo

The aft of the _Forward Unto Dawn _crept through space towards, hopefully, a planet with life.

Again.

Although their current predicament was not as time consuming as their previous one.

"There is no denying it Chief, "Cortana said, "This is the Sol System except there is no UNSC."

When they had first arrived here they appeared about halfway between Mars and Earth. What put up a red flag immediately is that Earth's Africa was not half-glassed or there at all. There looked to be little advancement in space, barely any satellites, no UNSC ships, and no Super MAC guns.

The worst part of this is that there was a giant, golden and white goat (llama?) headed to them. Through _space_. Also they were on a direct course for a populated settlement on said Earth.

The giant llama started talking to them which made Cortana and Master Chief question their sanity.

"Who are you? What is this? How did you get here?" they llama said once it was close enough.

Arceus was just sitting in the Hall of Origins since the universe seemed to be at as good a balance it was ever going to get at one point in time. That is until a ripple caused by Dialga and Palkia's incessant bickering brought forth a massive object easily three hundred meters in size.

Something that would easily destroy a large amount of humans and pokemon. He started to think of a way to destroy it until he sensed two intelligences inside the object. So he did what he thought was a sensible thing and went out trying to see what they were because they certainly weren't his.

When Arceus got there he was surprised to see a seven foot tall humanoid with both intelligences emanating from it. Arceus had to know what it was and if it was a threat.

"What are you?" Arceus decided to say first through telepathy.

The figure just stood there, at least to the untrained eye when really Master Chief tensed up because the llama talked to him but certainly not through space and not through radio contact. Master Chief decided to just say the real answer since this llama gave off a semblance of power.

"I," Master Chief stated, "am Master Chief Petty Officer one-one-seven of the United Nations Space Command."

Now it was Arceus' turn to be uneasy. He knew of the United Nations because the prospect of humans at peace with each other appealed to him. Being the Arceus he knew of said rank but why would a peace council have a soldier? Another thing that he did not understand about this human was that instead of the customary human name there was just a number.

Perturbed Arceus continued his interrogation while eyeing the gun the figure did not let go of. "What is this?"

"This," Master Chief replied, "is the aft UNSC frigate _Forward Unto Dawn_. Now troubled Arceus reluctantly asked his last question.

"How did you get here?" A female voice came from the suit answering, "I think I can answer that question."

Arceus was shocked because the earlier voice was assuredly male. "What my sensors got," the female voice continued, "is an unusually strong and volatile Slipspace portal. The radiation readings almost suggest that it was not a whole into Slipspace or rather an entirely different universe."

Arceus was now more confused than anything confuse ray could hope to achieve. Then it hit him, Dialga and Palkia were the beings of time and space. Something that could transcend both would have to be the result of their fighting.

As he was about to voice his realization the entire structure shuddered because now the ship was caught in the gravity well of the approaching planet.

"Well Chief," the female voice inside the suit said, "it looks like you're going to have an atmospheric insertion in nothing but your armor, again."

"Yeah, déjà vu" and with that the Chief just jumped to the planet below. Arceus was astounded and being the calm legendary pokemon he was could only say, "Damn. For a brick, he flies pretty good."

A/N: I absolutely had to put one of Johnson's lines in here. I have plans on trying to fit more in here except I may not be able too.


	3. Dying Arrangements

Chapter 3

As the Master Chief did an atmospheric reentry in nothing but his suit, again, he was heading to a little and almost unknown island off the coast of the continent that is known as Sinnoh. On said island…

Darkrai was in just another boring day on his own little Alcatraz. All that changed when a giant metal object came down from the sky. Darkrai's first thoughts about this were that either Deoxys or Rayquaza were having their odd fun.

This was quickly demolished when said giant metal object crashed into and completely destroyed Fullmoon Island. Little debris came his way and he paid little attention to it until he felt the peculiar presence of fear.

What made it peculiar was one; it was not Cresselia, two; there was no one except him on this island before the giant object crashed, and three; the sense of fear that Darkrai detected was, for lack of a better word, artificial and plummeting toward his island at a great velocity.

A large green object fell out of the sky right onto the island and impacted in the middle near Darkrai. When Darkrai recovered from said impact, he found that the large green object was humanoid and not moving.

When Darkrai moved closer to the object he thought, 'Damn. I thought I was badass but this is ridiculous. I hope it ain't dead because I haven't given anybody nightmares in a long time and I would love to do so to this thing.' The last thought Darkrai had with a devious grin if you could say he had a mouth.

As Darkrai was face-faceplate to the orange visor plate the object, or better person, slacked for a few milliseconds and then tried to put Darkrai in a choke hold. _Tried _being the key word here since the thing could not find Darkrai's neck. Darkrai, fearing for his life, tried a Dark Void on the creature only for it to slack for a second then shake it off.

Darkrai froze from shock long enough for the creature to get him into an arm lock. The creature then put his foot on Darkrai's back and proceeded to rip Darkrai's arms right out of their sockets.

Right before the arms gave Arceus arrived and said, "Stop! What are you doing?"

Darkrai looked on through the pain in fear because the last time he saw Arceus he was pissed at Darkrai. Master Chief let go of Darkrai's arms and looked at Arceus, studying him.

Arceus on the other hand asked Master Chief, "Do you want to return to your home?"

Master Chief pondered this for a minute. Choice A: Return home to a war stricken galaxy that he has nearly gotten killed in multiple times but it gave him a purpose. Choice B: Stay here in this strange universe that possessed weird creatures with odd abilities.

"Yes" was Master Chief's answer. Arceus looked gleeful at the answer as if he knew the choice already.

Arceus then said, "I can send you home but two of my children are acting up and I would like you to reprimand them. They are also the cause of your journey here."

"Wait Hold on a minute here!" said the Cortana from the Chief's armor. Cortana then jumped into the real world using holographic projectors on the armor.

Arceus and Darkrai knew of Cortana's presence but they expect her to be like this.

Cortana ignored their shock and rambled on, "So you mean that you want us to talk some sense into kids. Powerful kids that got us here."

If Arceus could snap he would of. "I got an idea, what I improve you two to be able to take on them?"

"Uh, no," was Cortana's answer, "I'm a crazy near death AI and he is a crazy near suicidal super soldier. We are fine as we are."

"What if I could improve you both even more, including healing all deficitcies?"

Cortana halted and Master Chief froze up from this revelation and Darkrai was trying to slink away.

Arceus didn't even look away while he said, "Darkrai, stay here I have a task for you."

Cortana went back into the Chief's armor and the two had a private conversation.

"I say we do," said Cortana.

"We don't even know what he would do." said the Chief.

"Well we won't know unless we ask."

"Fine but only a trial run."

Cortana then spoke up and said, "Show us what you mean by 'improve'."

Master Chief was covered in a white glow and when that receded a Gardevoir and a Lucario were in the Chief's places. Although they were different: The Gardevoir had psychic abilities equal to that of Legendary and its entire body was blue. The Lucario was easily six feet tall and he was olive green where a Lucario would be blue and the spikes were all black. The Lucario also had piercing orange eyes and it just radiated strength, aura-wise and physically.

Both looked on in marvel of each other until Arceus spoke up saying, "Of course the human would still retain his human form so that you could travel easier."

Cortana was amazed at her new form and reveled in the fact that she was beautiful and she had a body. John walked up to a tree and gave it a punch snapping it as if it were a grunt neck.

"This form is as strong as my regular one. How is this an improvement?" said John.

John had a feeling in his gut and dodged a rock at the last second. More rocks followed the first and John dodged all with ease until they stopped. John looked to who had thrown the rocks and saw it was Arceus.

"See? Your abilities have been improved upon ten-fold. Now if you accept then I can point you towards which path you should take to return home."

Before John could answer Cortana answered, "Yes!" then started spinning around.

John sighed and then said, "I conclude with my partner. Now any information on the mission would be helpful."

Arceus gave laugh and then said, "Good, now three things: One, to get off this island wait until the boat stops by. Two, take the gym circuit in Sinnoh and your mission will come to you. And three, Darkrai is coming with you."

Darkrai reeled back shocked and then said, "You want me to do what now?"

"I," Arceus explained, "want you to guide these two in this world and help them get accustomed to it. Both are impervious to your nightmare abilities and they need to learn how to control their power. You will also do as the Lucario commands including fighting in these gyms. If you do not then your last punishment will pale in comparison to the one you would receive if you do not do this. Do I make myself clear?"

Darkrai gulped before answering, "C-crystal."

Arceus gave a nod to everyone and then disappeared off into a portal. Darkrai gave a sigh before saying, "How we got to worshipping and fearing a llama I'll never know."


	4. The Penetrable Defense

Chapter 4

Disclaimer: I do not own Pokemon or Halo

It had been a week since Arceus had left Darkrai, John, and Cortana and there were definitely some changes. John learned to shift from Lucario to human, Cortana had mastered her massive psychic abilities in less than three hours, and John could use aura equal to that of a master.

John had found some Pokeballs earlier and managed to put him, Darkrai, and Cortana in their own after Darkrai had to explain their purpose and how to use them. It had been discovered that John's armor had turned into his Lucario skin and that he could manipulate his shields as well as his aura.

All three stood on the coast of Newmoon Island watching the boat come in and all boarded, though there was some apprehensiveness due to Darkrai, Cortana, and John's appearance.

Once the three reached Canalave City John returned Darkrai and Cortana and headed directly to the gym to inquire about the gym circuit. When he got there was only a man leaning on a statue present.

John walked up to the man and asked, "Do you know where I can ask about the gym circuit?"

The odd man looked up and said, "Why would you want to know?"

John answered, "I would like to challenge the circuit."

"HA!" was the man's reply. "If you do want to challenge it though then just walk into the gym and go challenge the leader. I warn you though it would not be a good idea to take on this gym first but if you think you can do it go ahead."

John walked off and towards a red-haired man with a shovel. He was just a little smaller and less muscular than John.

The man said, "I am Byron the Steel-type gym leader. Are you here to challenge me? If you are then I warn you about my impenetrable defense!"

John merely nodded and took position opposite of Byron on a battlefield. John and Cortana had earlier been explained the rules of a pokemon battle so that is how John knew so much.

John then yelled across the field, "Is this battle in anyway recorded or watched?"

Byron Looked curious before saying, "No, not that I know of but why would you ask that?"

"I have a very unusual team."

"Well then let's get down to it!"

Byron threw up a Pokeball while yelling, "Let's go Bronzor!"

John only raised his hand and let out Darkrai who cackled at the sight of a Psychic type.

Byron looked only slightly fazed but yelled, "Bronzor use Iron Defense!"

John just stood there and said, "Darkrai, prepare for a combo move."

Bronzor looked to get stronger while Darkrai looked more focused.

Byron the said, "Use Gyro Ball!"

Bronzor raced forward spinning and when he was close to Darkrai John said coolly, "Dark Charge Beam.*"

Darkrai unleashed his combo move before Bronzor could hit him and fired the powerful attack nearly knocking out the Bronzor.

Byron had a surprised look on his face but said, "Bronzor use Flash Cannon."

Bronzor fired it quickly and Darkrai dodged instinctively but was hit along his right side.

John stood there unaffected by Darkrai getting hit which greatly unnerved Byron.

John then said, "Jump into the shadows and fire numerous Charge Beams."

Darkrai did just that and Bronzor had no time to react as he was hit ruthlessly from everywhere by Charge Beams. Bronzor dropped to the ground knocked out.

Byron returned Bronzor and the let out a Bastiodon who gave out a mighty roar.

John said, "Darkrai, sit this one out."

Darkrai moved to float beside John who let out Cortana. Byron raised his eyebrow at Cortana's color but gave no other indication of intimidation.

Byron then said, "Bastiodon use Iron Defense!"

Bastiodon did as Cortana psychically talked with John.

'_Chief, what do you want me to do?' _John relayed his plan to her while giving the Bastiodon a cold, calculating look.

Byron then said, "Bastiodon use Take Down!"

Bastiodon raced forward to hit Cortana but was electrocuted, only not by Cortana. Byron wondered what happened until he saw sparks all throughout the air and Cortana showing the telltale signs of using Psychic.

Byron gave a laugh before saying, "So you're making static electricity? That won't stop Bastiodon!"

Bastiodon gave a different answer as he keeled over from being a living lightning rod.

John then said, "Finish it."

Cortana then loosed a Psychic that knocked out the Bastiodon.

Byron looked shocked but he quickly recovered saying, "You beat Bastiodon. Well I still have one more left."

Byron the returned Bastiodon and let out a Lucario.

John then said, "Cortana sit this one out."

Cortana moved to be beside Darkrai as John stepped into the arena and shifted into his Lucario form.

Byron and his Lucario gaped but recovered quickly with the Lucario saying, "I was hoping for a challenge."

Byron did the unpredictable next and said, "Lucario you're in charge! Take him down!"

Lucario raced to John intent on a Force Palm and he hit … John's shield.

Lucario was shocked but was even more when John delivered a roundhouse kick which sent Lucario flying.

Lucario then fired an Aura Sphere once he landed and John copied his move. The two Aura Spheres met in the middle and neutralized each other leaving a lot of smoke.

Both Lucario combatants rushed forward using their Aura Vision to exchange blows with each other. The smoke cleared shortly to find both using Close Combat. John was much stronger and faster but only limited himself somewhat to not kill his opponent.

When the two pulled away from each other both could be seen with large bruises. Lucario raced at John with an Iron Tail which John defended himself with a Metal Claw. They stayed frozen in place trying to get the upper hand when John let some more strength into his defense which threw back Lucario.

Both charged up and fired Aura Spheres and had the same result as earlier until John was seen powering up a powerful attack. John let out a Hyper Beam which Lucario barely missed with a Detect. While John was frozen in place Lucario came forward with an Iron Tail and scored a hit on John's ribcage.

The result shocked everyone as it was Lucario's tail that broke under the stress due to John's carbon-reinforced skeleton.

Lucario backed off only to see an Aura Sphere come for him. Lucario then used a Bone Rush to redirect the Aura Sphere back at John. John braced for the attack and took the sphere and was hit again by Lucario coming in with a simultaneous Bone Rush and Close Combat.

John took quite a few hits but was able to block or dodge most. John then lunged with a Metal Claw and struck Lucario's head on causing Lucario to stumble backwards. Both looked at each other and came at each other with Bone Rushes. Then both pulled a fast one and used Extreme Speed(pun intended) to boost themselves and they disappeared momentarily.

They reappeared behind each other facing away. John relaxed as Lucario fell to the ground from exhaustion.

John shifted back into his human form as Byron returned Lucario and came forward to John.

"Well, I now know why you wanted this battle secret and what's more you won. I gladly present you with the Mine Badge."

Byron then handed over the badge to John who put it in one of his pockets. John turned to leave until Byron said, "By the way did you use to work in the mines? You have the build of someone who has."

John didn't turn around as he replied, "No, I'm just a soldier who has seen more than his fair share of action."

With that John took his leave with Cortana and Darkrai close behind him.

Byron gained a new respect for John and then sent out a message to his fellow gym leaders:

_There is a new trainer coming around. A soldier to be precise._

_Better start making those white flags._

A/N: Lucario is awesome! He deserves to be in more than one gym and the Pokemon League. *Dark Charge beam is a Dark Pulse and Charge Beam.


	5. Intimidation: Pansy Style

Ch.5

Disclaimer: I do not own Pokemon or Halo

John walked through Canalave City straight to the exit that would lead to Jubilife. When he and his companions reach the body of water John looks to Cortana which is enough to say, "I need help."

Cortana grabbed John in a psychic grip and flew over to the opposite shore. The opposite shore though was easily as big as the English Channel and therefore took Cortana the better part of the day to get him and her all the way to shore. Darkrai floated on his own and sent out the occasional Dark Void to any wild Pokemon that got too close.

When shore was reached Cortana lay on the grass and said, "If you need me it had better be an emergency else I won't be the only female here."

Darkrai backed off from her while John ignored her and got to work on making a campfire. Once he had gotten all the wood, he used a nearby irregular rock and a combat knife he had found to spark the fire and proceeded to cook a Buneary that had been a little too unlucky for its feet.

The meat was cooked quickly due to the Chief's excellent survival skills and a full meal was had by him and Darkrai. Darkrai finally could not help and decided to get some information.

"So, were you able to resist my Dark Void?" he asked.

John gave a long hard stare at him as he said, "If you can survive that amount of exhaustion for three days straight in a constant warzone then what you pulled was no big matter."

Darkrai shut up and looked away chilled to the bone at the tone this conversation was getting too. John finished his meal and quickly fell asleep without another word.

Darkrai knew he couldn't inflict nightmares on his two companions but he did want to try another of his tricks, dream-peering. Darkrai first decided to look inside of Cortana's dreams.

Cortana's dreams held few things being namely:

John

The Halos

Her time with the Gravemind

A complex and headache-inducing amount of algorithms, formulas, and calculations mixed with varying languages.

Darkrai got out of her dreams confused but disturbed about the Gravemind. To him though one good thing came out of this, a new idea for nightmares. Darkrai decided to look into John's dreams and what he saw truly horrified the embodiment of nightmares.

All around in the dreams Darkrai could see odd, murderous creatures, parasites, blood, technology, and killing always killing. Thousands die at the hands of John those who look similar to John could be seen in replays of their deaths that went in continuous loops.

Darkrai got out as soon as possible and figured that these two, especially John, had things no other sentient being should see. Darkrai moved over farthest from the fire, which was now embers, and settled him in for some sleep.

At the crack of dawn John was up and already waking his companions as well as cleaning the campsite. He got the entire place clean in a matter of minutes and the trio moved on with their journey into Jubilife City.

In Jubilife City there were a few incidents. One being a couple of robbers trying to get past John. They were dealt with extreme prejudice and wound up being hauled onto stretchers to the Police Station. Another incident was the clowns trying to sell Poketchs to John. At first he declined and they were increasingly persistent to the point of getting on his back to bug him. The end result was a broken clown and a felled lamppost.

The final incident though crowned them all as two people in odd clothes and blue bowl shaped haircuts tried to hold up an old man and a little girl with Pokemon. John rushed in and neutralized (killed) the Pokemon in two hits and the broke every non-vital bone in the two grunts bodies.

The old man came up to John saying, "Uh, thank you for the assistance is there anything I can do to repay you?"

John shook his head and moved on while the old man gaped at Darkrai and Cortana. John reached the limits of the city when more of those people in odd clothes with weird haircuts surrounded him. A man with a V-shaped haircut approached John saying, "You interfered in the affairs of Team Galactic and for that you will pay."

Said man released a Toxicroak while the others released Dustoxs, Glameows, and Stunkys. The Pokemon surrounded the trio and John said, "Darkrai, be merciless on these ones, human and pokemon. Take one-third while Cortana and I take on equal amounts."

Darkrai grunted in affirmation and John shifted into his Lucario form surprising the people surrounding him. He launched forward at full strength and speed and entered Spartan Time.

A Dustox, two Stunkys, a Glameow, the Toxicroak faced off against him. The Dustox he jumped up to and ripped its wings off before punching through the exoskeleton. The Glameow tried to use Scratch on him except it encountered his shields and was then grabbed by the tail and hogtied with it.

The Stunkys ran at him for a simueltaneous takedown except one was gutted with an Aura Sphere and the other was impaled on the Chief's Bone Rush. The Toxicroak was smarter and attempted a Poison Jab only to realize Lucarios are part Steel type and immune to Poison. John used Force Palm on its smug face and flung i tree.

The Toxicroak recovered quickly and made to use Brick Break but Master Chief used Detect to slip by and encountered a second Brick Break to the gut. The Chief shook it off easily and lunged forward with a simple, Chuck Norris style roundhouse kick. The effect was immediate as the Toxicroak crashed through two trees and broke the neck of the grunt it landed on.

Saturn made a run for it once the fight began so it was four grunts versus Master Chief. The poor grunts. Master Chief made his usual Bone Rush but manipulated the aura to take the form of a Covenant Energy Sword.

John dashed forward too fast for them to react as he impaled one grunt through the heart then whipped out the blade catching a second grunt through the face. John then dislodged the corpse by flinging the blade at the remaining two causing them to duck.

Only it was a diversion as John ran up too both grunts and put his palms on their heads and used Force Palm. The heads of the grunts exploded as if they were shot point-blank by a high-powered rifle.

The Chief turned to see Cortana and Darkrai finishing off their grunts and no sign of the leader. John kept note of this group and shifted back to human and moved on towards Oreburgh City.

Outside of the city limits they camped again but their meal consisted of a Starly each. Sleep came quickly to all as none worried about their engagements with Team Galactic.

They should've though because a purple four-winged bat headed in Northeasterly direction back to its master. Once there the camera strapped to it was removed and the video examined by the leader of Team Galactic.

"Hmm," said Cyrus, "It seems we have a new obstacle in our midst; one that could throw off our plans. Mars!"

A red haired woman emerged from the shadows saying, "Yes, master."

"I want you to take an assault squad but no Pokemon, just humans and give them the new weapon R&D came up with."

"You mean guns sir?"

"Yes, I want you to kill these interferers and record it; I want to see the effectiveness of these guns."

"Yes, master."

A/N: The only reason I have a cliffhanger here is so that I can put a large amount of fighting in the next chapter.


End file.
